Malaria is one of the major public health problems of Bangladesh. We investigated the mosquito populations infected with malaria parasites in a malaria-endemic area Chakaria, Bangladesh, where Anopheles dirus and Anopheles minimus are the principal vectors. Anopheles mosquitoes were collected with a CDC miniature light trap from inside households in June 2007. A total of 868 mosquitoes were collected, among which females numbered 669 (77.1%). The species of female Anopheles mosquitoes were identified morphologically, and 651 were A. minimus and the remaining 18 were other Anopheles species. Malaria parasite DNA from individual female mosquitoes was extracted and distinguished using the microtiter plate hybridization (MPH) technique targeting the 18S rRNA of human malaria parasites. Nineteen mosquitoes were malaria parasite positive: 12 for Plasmodium falciparum, 1 for Plasmodium vivax, and 6 for both P. falciparum and P. vivax. This is the first time that the MPH technique was used for distinguishing malaria parasites in mosquitoes and the first report from Chakaria. Our results may contribute to planning and assessing malaria control strategies in Chakaria.